Sonic Crystal
by DollarLollar
Summary: Eggman gains an unlikely new assistant while Sonic and his friends try to stop them. They encounter a Lynxe cat who was one of Eggman's prisoners. After rescuing the girl from danger, the gang has an eerie feeling that something is a miss. Their world begins to change around them as a new weapon is unleashed onto the world.
1. Chapter 1

*****((Author's Note))*****

**((This was an old fanfiction I found while cleaning out my room. I decided to re-write it here because it had a storyline, but was in a 10 year old grammar/format. Enjoy the messed up fanfiction that is this one guys.))**

Another one of Eggman's robots had been defeated by none other than the blue blur himself. As the evil scientist was groveling, in his own self pity, he heard footsteps behind him. He turned to see a woman, tall in stature, with her arms crossed. She was wearing a lab coat, with a grey turtleneck sweater over her charcoal black skirt. Her heel kicked the discarded part of the robot Eggman had built.

"Snively was right. You really are pathetic." She scoffed, moving her white hair away from her face.

"Snively left years ago… and who might you be?" Eggman asked confused by her being in this random place.

"Faust is my name and Let's just say that I am here to help." Faust replied to him while holding out her hand.

Eggman hesitated before taking her hand. "Why do this?"

"An eye for an eye. That blue rat took something from me and I want it back."

Meanwhile Sonic and the gang were heading back after having another victory. Tails flew his Tornado One plane, while knuckles and Sonic stood on the wings of it. As the plane landed Sonic remembered something he snagged for tails to look at. He handed the flash drive to his fox friend as they got off the plane. Tails noticed the flash drive looked to be more advanced, but there were runes on it that he couldn't pick out. While Sonic and Knuckles began chatting, he went inside to see what was on it. As Tails put the drive into his computer it instantly emitted a distress beacon. A map was pointing to a location with longitudes and latitudes on it.

"What was on the drive little buddy?" Sonic asked curiously while walking inside.

Tails showed him the map, "It looks like a rescue mission on one of Eggman's bases." and Sonic took the map.

"Then we should get going. It should be easy enough while he's building another robot." Knuckles held the door open, awaiting them to exit.

"Well it is strange. It's at one of the abandoned bases." Tails explained and Sonic knew that this was too familiar.

"So, it's a trap for us then? What else is new?" Sonic chuckled and headed out. "I can probably deal with this trap on my own. You guys can relax for a bit."

Before Tails or Knuckles could say anything Sonic had left. Tails sighed as he began decoding more of the file. Knuckles noticed the flash drive had runes on it that he had only seen in one place. Sonic had arrived at Eggman's abandoned base and it definitely was abandoned. The metalic building were rusted and the structure was falling apart. Vines had started to cover some parts of the building while he made his way through the rubble.

"Why would someone be here?" Sonic asked aloud, but noticed a large robot in front of him. "This looks like Egghead's, but somethings different..."

The robot was a metallic silver with what looked to be ivory or granite mixed in with the metallic armor. Its arms were slender, but its body was big at the top and smaller at the bottom. The robot's head was a diamond shape with a helmet that had a hole in it. The robot had been there for a long time because it was completely encased in vines and leaves. Sonic put his finger to the robot's armor and noticed the accumulative dust that was on it.

"This can't be Eggman's… it's too old." He began to hear a voice coming from the corridor behind him. "Hello?"

Sonic began following the voice, every turn the sound made itself known in a different location. He followed the voice, not noticing the walls becoming darker, and then the voice getting louder. The voice began to cry out for help and Sonic picked up his pace. When he got closer to the voice it changed into different disorenting people crying and weeping. Sonic still moved forward until he reached a broken door. When he entered the room the voices ceased abruptly.

A shiver went up his spine as a strange feeling went over him. "That was ...weird…" he bumped into another robot from the first room. "Another one?" Sonic noticed as the light peeked through the room was filled with them. They all pointed to the wall to his left. Sonic made his way there and noticed they were cells. All of them were open except for one that was locked.

"This must be it."

He looked around for a key of sorts to open the cell when the light peering into the room made something on the middle robot glisten. "Ah!" Sonic dashed up to the top of the robot and saw the helmet it wore had an emblem on it. "Thank you my friend! I will return it to you soon." He replied, taking the diamond piece out, and hurrining back to the cell. Sonic put the diamond ensignia into the cell keyhole. It unlocked and the cell door slid open and crumbled.

Sonic was surprised, "I-it's a girl!" and he rushed to see if she was alive.

The girl was a lynxe cat with rose gold fur and dark brown hair. She was wearing a faded teal shirt and boots. Around her neck was a lanyard with a name on it. _Crystal_. Sonic assumed it was her name as he realized she was unconscious. "Okay, let's get you out of this place." Sonic said, picking her up bridal style, and running out of the facility.

"So, we just let him go?" Eggman says, perplexed by his new assistant's plan.

She smiles devilishly, "Patience is a virtue doctor." and began pulling up a blueprint. "You thought of a robot army have you not?"

Eggman nodded as he scanned her plans. "This is a strange biotechnology...these theories haven't been tested yet!"

"Oh they have made progress, but the experiments were deemed too inhuman. That's where we step in."

Sonic arrived back at home and Amy took the girl he found to get examined for injuries. Tails was noticing that Knuckles knew the markings or runes on the drive that were now on the screen. Knuckles had seen these before, but not on Angel Island nor Babylon. It was a forgotten nation that had been said to be extinct for eons. Nevertheless, he tried to decipher the messages on the screen to the best of his abilities. Sonic walked in to the wall of HQ now with writing on it. One was their native language, babylonian, and another that seemed to be gibberish. He tapped Tails on the shoulder.

"Uh, why are we writing on the walls?"

"It'll wash off. We just needed more space." Knuckles explained as he was reading from a journal tails had written in.

"So, what did you find?" Tails asked Sonic about the mission.

Sonic scratched his head, "I-uh, found a girl in a cell. It was also filled with these old robots and runes like what it on the screen" and heard a crash outside the door.


	2. Chapter 2

*****((Author's note))*****

**((Here is the next one. Enjoy you beautiful people!))**

Sonic, Tails, and Knuckles rushed out the door to find Amy holding her hammer up steady. Their sights shifted to the girl Sonic rescued armed with a bow and arrow aimed at their pink friend. Sonic noticed she was shaking and her side was bleeding. She looks terrified...maybe this wasn't the best of ideas... Sonic begins to walk towards her, causing the Nynxe to steady her aim towards him, and he holds his hands above his head. Sonic Looks at Amy and she lowers her hammer while Tails and Knuckles just watch.

"You're okay. You're safe." Sonic says calmly as the girl begins to lower her bow.

She notices she is not in the same place she was before. She begins to speak with her words shaking. "W-why am I here!?" and backs away from Sonic.

"We found a distress beacon coming from your location." Tails replied, noticing her ears go down hearing those words.

"You alright?" Sonic asked her as she looked to be thinking of something intensely.

"How?" She falls to her knees, "D-did he-" then wenches in pain while grabbing her side.

Sonic motions for someone to get the first-aid kit and knuckles does so. "Hey, take it easy. You're hurt." He kneels down in front of her. "My name's Sonic. What's yours?"

She hesitates and notices his looks sincere. "Crystal..."

"Well, Crystal welcome to our home! You need anything just ask." Sonic replied holding out his hand.

"I-is this a trap? Will you zap me or something?" Crystal asks, skeptical of taking a stranger's hand.

"The only zapping we'll be doing is defeating Egghead's robots." Sonic explained while chuckling at her statement.

"Egghead?" Crystal was confused and Tails explained.

"Dr. Eggman is who he meant. This guy roboticized people for his Eggman Empire and we thwarted most of his plans so far."

Crystal stood up, Sonic retracted his hand, and Tails noticed her change in tune. "You are freedom fighters then?"

"Yeah, I'm Tails and this is Amy."

Sonic pointed to Knuckles as the echidna was back with the medical kit. "That blockhead over there is named Knuckles."

"I'm not a blockhead all the time. I still do some treasure hunting, but not often." Knuckles replied, handing Amy the kit.

"Will you let us help you?" Amy noticed that Crystal was calmer now and less freaked out.

Crystal nodded, "Y-yes, sorry for the skirmish..." and she began to walk with Amy.

Sonic sighed in relief that the situation didn't escalate any further. Knuckles noticed there was a lanyard on the ground. So, he picked it up. "Wait a second..." Knuckles stated, walking back inside.

Sonic and tails followed. "What's wrong?"

"The markings on her lanyard match the ones on the drive." Knuckles explained, aligning it with the writing on the wall.

"It says crystal in plain english." Sonic explained while his two friends looked at him as if he was mad.

"Wait." Tails started and Knuckles finished. "You can read this!?"

Knuckles shoved the ID in his friend's face. Sonic noticed the words were no longer there as they were when he found her. Sonic blinked in shock and replied in disbelief. "I-it now looks like gibberish."

"We need answers and it looks like Crystal may have them." Tails explained to them both.

**{Crystal's Flashback}**

Crystal made her way through the doors of the academy. She noticed all the students going to and from their classes. Her brother had just finished his final for one course when she spotted him down the hallway. Her brother greeted her with joy as they embraced in a hug. Crystal followed him to his own lab where she noticed all of his new ideas. Robots and her friends were there, smiling, laughing over someone mixing the wrong chemical, and just being happy. She saw how the clinical trial that her brother had made for prosthetic limbs was a success. The head of the medical department wanted him to do more and he did to help others around him.

"Here look at this!" Her brother said in excitement while handing her a piece of paper.

Crystal noticed the writing was in an ancient text. "Wait.. this is-"

"The origin language! I have almost deserved it with your help!" Her brother rushed to the computer and pulled up the monitors. He moved the open windows out of the way until he reached one. "This right here was said to be a robot made by the Origins. Could you translate for me what it says?"

Crystal smirked, "Healing is found in these grounds. Healing is where the metal is bound." and stopped to pounder what that could mean.

"I was right! They used biotechnology, like with what we are using now."

"Brother it may be something else. Remember, they were a thriving nation, but disappeared overnight."

Her brother sat down on his chair and spun it around. "I know that is another theory, but what if they found a way to make it possible to revert the injuries that a person suffered form?"

"Well, you'll have to test that theory? Won't you?" Crystal chuckled as the door opened in the laboratory.

**(End of Flashback)**

Crystal woke up from her dream. She noticed the room was changed then realized where she was. At the Freedom Fighter's Headquarters. Where they would stop plans made by Dr. Robotnik or Eggman as he is now being called. He uses the powerful mind that he possesses to roboticize his own people and take over more and more land to build his empire. Crystal couldn't imagine someone using technology for that kind of destruction. However, she'd seen it before in her homeland. The government getting power hungry, colonizing other parts of the country as they said it was their duty to invade other nations. Using weapons that were intended to help people for devastating and demolishing cities and countries. She'd seen her once powerful nation crumble under one ruler. Crystal noticed she was bandaged. They held up their word here so, she guessed they could be trusted. Amy walked in with a trey of food and handed it to her.

"Morning! Here is your breakfast." Amy said in a chipper tone.

Crystal blinked for a moment, "Is it poisoned? Also, how are you this happy in the morning?" and Amy laughed at her statement.

"Of course it's not poisoned. I am just a morning person that's all"

Sonic walked in the door as Crystal began eating her breakfast. He noticed the two chatting away and actually saw how amy could make Crystal feel safer here. Once the two were done with one topic they saw him leaning on the doorframe. Amy smiled as she took Crystal's empty trey walking out. Crystal noticed how the blue hedgehog was holding her lanyard.

"How did you get that?" She asked him.

"It fell off you when you were aiming at me with your bow." He replied tossing it to her.

"Wait...you're just giving it back?"

"Yeah it is yours after all." He explained and Crystal could tell something was a miss.

"What is it that you want?"

"We need your help figuring out something." Sonic replied, then she answered his question.

"If it's about the language on the drive, then that is a no..." Crystal crossed her arms and faced away from him.

The blue hedgehog was shocked, no one had said no before to him wanting help. Well, except for Shadow, Knuckles occasionally, and his enemies.

"O-okay, that is fine. You need time, but I got that drive from Eggman's base. If he has discovered another way of expanding his empire then he'll do it." Sonic explained, hoping she would change her mind.

"He can't read that writing anyway, trust me." Crystal stated while getting out of bed.

"Egghead's got an IQ of 300 so, he may be able to."

"My brother had the same IQ and he couldn't crack it until I did for him." She began to put on her shoes and the sole detached from the entire shoe. She grumbled and popped back on the bed.

"You need new shoes?" Sonic asked her, quickly changing the question.

"Indeed captain obvious."

He chuckled and responded to her. "Then would you like to get new ones? No cost at all."

Crystal shot up from her bed with a skeptical expression. "No cost?"

"Well, there is one cost." Sonic shrugged and smiled with his answer. "Your trust."


	3. Chapter 3

*****((Author's Note))*****

**((New chapter new information! You people enjoy and I may even draw some stuff because I found my cringy old fanart. If you want to see some drawings they will be on my tumblr. ))**

Crystal was walking with Sonic outside a shop and he was puzzled to why she didn't ask for him to hold her bags. Normally Cream or Amy would ask, but Crystal didn't. He tapped her on the shoulder while Crystal was deep in thought. Crystal couldn't understand why these people were being so nice to her. Others wouldn't help her so, why would they. Sonic tapped her shoulder again, now a bit worried.

"Hey, Crystal. You okay?" Crystal snapped out of her thoughts.

"Huh?"

"You were daydreaming and almost walked into a tree." Sonic stated as they moved away from the tree.

"Oh, I was just wondering something." She responded, looking down at her new dark teal boots.

Sonic noticed her scanning her bags of clothes. "You wondering if you have to pay for those?"

"No, not that." She said pulling out a mint blouse with a grey zipper in the middle. She unzipped the blouse, put it over her tattered shirt, then zipped it up. She then discarded the rugged clothing underneath her new blouse into the trash can. Sonic blinked in shock of what just happened. "Why are you being so nice?"

"Why not?"

Crystal turned to face him. "Why not? What happens when someone you are kind to stabs you in the back?"

"Then you keep moving forward. Eventually you'll find friends around you that won't do that." Sonic answered, noticing her expression change. "Let me guess. You've never had someone stand by you?"

Crystal nodded, "With what is on that drive you found." then sat down on a bench. "Everyone either leaves or tries to kill me."

Sonic sat down next to her. "Well, we won't do that to you because we know what it's like."

"You know what it is like?" She stood up and held out her hand. "Then come with me."

"Alright, do you want to get there fast?" Sonic asked while taking her hand.

"Sure, why not?" She was confused by the question as he picked her up, bridal-style, and began to run.

While the two went to the ruins Faust was reading over plans and noticed the cell behind her. She opened it and saw Snively in chains. He flinched, seeing the woman walk toward her. She grinned, leaving a note on the ground. Snively read in horror as the note informed him of her next plan. Eggman came up to her and she went to one of the monitors. Faust began typing in something then entered in the command. The monitor showed a male nyxe shackled to the wall with others around him. His white hair in a disarray and outfit ruined by the experiments.

"Should we begin phase one?" Faust asked, and Eggman nodded in agreement. "Splendid."

She pulled the lever beside her and the machines in each of the holding facilities turned on. Blood curdling screams were heard throughout the chambers. Flashing lights danced across the monitors as she observed the experiments falling one by one to the ground. "Now for phase two."

Sonic and Crystal made it to the old abandoned base. Sonic looked around and noticed a figure walking in the distance. it was one of the robots from the ruins.

"The robots are moving now." Sonic noticed while he put her down.

Crystal whistled for the robot and it walked up to them. This one was towering over 10 feet tall and was of similar structure to the others.

"The ruins and abandoned laboratories you find here were form the Original people who once lived here. Eggman could have used this base, but abandoned it. He probably didn't know how the machines worked around here. These robots are apart of what's left."

The robot kneeled down to meet her at eye-level. "These were the weapons used for that destruction, but they weren't meant for that."

Crystal took the diamond shaped gem off her lanyard and held it up to the robot. "They are meant to heal the lands..." She said an incantation as her the robot's eyes turned a calming lavender. "Go and help these lands grow and flourish."

The robot stood up, began walking away, while grass grew around its footsteps. Crystal put the gem to the ground beneath her and a tree sprouted up in between them as tall as the robot.

"So, the gems control the robots?" Sonic asked and she nodded.

"Yes. The robots respond to the host of the gem. This can be used for growth and destruction." Crystal explained as she held her hand to the tree and it decayed to ash. "That is what is mostly on the drive you found."

"Mostly on it?" Sonic said while watching her create a field of young trees beside her.

"The rest is something I don't even know." She said putting the gem back on her lanyard. "My brother never told me that part."

"You have a brother?"

"Had a brother...he went missing when Faust found out he was trying to erase his work for biotechnology." Sonic put his hand on her shoulder.

"I'm sorry. It must have been hard." He said and the two started walking. "I know what it feels like to lose your sibling...I lost mine when sonething bad happened..."

Crystal looked at him. "Sorry to hear that. He and my sister went missing when the multiverse reset itself"

Sonic stopped moving, "You know about the multiverse?" and she nodded.

"The Prime Zone is the name...I think. It looks like long intertwining roads. Each road leads to a different reality."

"Yeah, well you're talking to one who travled on it. My reality was reset after Eggman caused a super genesis wave." Sonic explained and Crystal stopped walking.

"He did what?" Crystal was shocked that a weapon could be built with such magnitude.

"He made a weapon so powerful it reset my world."

"Faust is working with Eggman. So, if he has the tools to do that then they have to be stopped."

Sonic was confused, "Why? What happens if it's reset again?" and she began to explain.

"Think of it like a video game except with only three lives. If you have already died two times and then die again. It's game over and there is nothing left." She explained further. "If the reality is reset too many times then it can collapse in on itself. It can lead to no realities resetting at all and a quantum abyss filling an endless void."

"Wait, WHAT!?" Sonic was cunfused and also slightly understanding what she explained.

Crystal sighed in frustration. "It is like this. Timelines or worlds with the multiverse is supposed to be natural. Whenever someone creates something that disrupts the multiverse it resets itself. The dimensions/realities are reset, but in a disarray of sorts because it wasn't the right time. So, it creates alternate realities so, the multiverse can be stabilized." Crystal Looked at him with saddened eyes. "That's why I lost my brother and everyone else. I'm sure you've lost more than family as well."

He put his hand on her shoulder and smiled. "Then let's not let it reset again."He looked at her with confidance. "We'll make sure of it."


End file.
